Comparative EST analysis provides insights into the basal aquatic fungus Blastocladiella emersonii

BACKGROUND: Blastocladiella emersonii is an aquatic fungus of the Chytridiomycete class, which is at the base of the fungal phylogenetic tree. In this sense, some ancestral characteristics of fungi and animals or fungi and plants could have been retained in this aquatic fungus and lost in members of late-diverging fungal species. To identify in B. emersonii sequences associated with these ancestral characteristics two approaches were followed: (1) a large-scale comparative analysis between putative unigene sequences (uniseqs) from B. emersonii and three databases constructed ad hoc with fungal proteins, animal proteins and plant unigenes deposited in Genbank, and (2) a pairwise comparison between B. emersonii full-length cDNA sequences and their putative orthologues in the ascomycete Neurospora crassa and the basidiomycete Ustilago maydis. RESULTS: Comparative analyses of B. emersonii uniseqs with fungi, animal and plant databases through the two approaches mentioned above produced 166 B. emersonii sequences, which were identified as putatively absent from other fungi or not previously described. Through these approaches we found: (1) possible orthologues of genes previously identified as specific to animals and/or plants, and (2) genes conserved in fungi, but with a large difference in divergence rate in B. emersonii. Among these sequences, we observed cDNAs encoding enzymes from coenzyme B(12)-dependent propionyl-CoA pathway, a metabolic route not previously described in fungi, and validated their expression in Northern blots. CONCLUSION: Using two different approaches involving comparative sequence analyses, we could identify sequences from the early-diverging fungus B. emersonii previously considered specific to animals or plants, and highly divergent sequences from the same fungus relative to other fungi

Extracytoplasmic function (ECF) sigma factor ^F is involved in Caulobacter crescentus response to heavy metal stress

Background: The -proteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metals in these sites. It has been reported that C. crescentus responds to exposure to various heavy metals by altering the expression of a large number of genes.Results: In this work, we show that the ECF sigma factor F is one of the regulatory proteins involved in the control of the transcriptional response to chromium and cadmium. Microarray experiments indicate that F controls eight genes during chromium stress, most of which were previously described as induced by heavy metals. Surprisingly, F itself is not strongly auto-regulated under metal stress conditions. Interestingly, F-dependent genes are not induced in the presence of agents that generate reactive oxygen species. Promoter analyses revealed that a conserved F-dependent sequence is located upstream of all genes of the F regulon. In addition, we show that the second gene in the sigF operon acts as a negative regulator of F function, and the encoded protein has been named NrsF (Negative regulator of sigma F). Substitution of two conserved cysteine residues (C131 and C181) in NrsF affects its ability to maintain the expression of F-dependent genes at basal levels. Furthermore, we show that F is released into the cytoplasm during chromium stress and in cells carrying point mutations in both conserved cysteines of the protein NrsF.Conclusion: A possible mechanism for induction of the F-dependent genes by chromium and cadmium is the inactivation of the putative anti-sigma factor NrsF, leading to the release of F to bind RNA polymerase core and drive transcription of its regulon.</p

BayGO: Bayesian analysis of ontology term enrichment in microarray data

BACKGROUND: The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. RESULTS: BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. CONCLUSION: The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

<p>Abstract</p> <p>Background</p> <p><it>Xylella fastidiosa</it>, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, <it>X. fastidiosa </it>needs to cope with nitrogen limitation in its natural habitat.</p> <p>Results</p> <p>In this work, we performed a whole-genome microarray analysis of the <it>X. fastidiosa </it>nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the <it>rpoN </it>null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ⁵⁴-dependent manner. A more complete picture of the σ⁵⁴regulon was achieved by combining the transcriptome data with an <it>in silico </it>search for potential σ⁵⁴-dependent promoters, using a position weight matrix approach. One of these σ⁵⁴-predicted binding sites, located upstream of the <it>glnA </it>gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ⁵⁴-dependent promoter.</p> <p>Conclusions</p> <p>Together, these results show that nitrogen starvation causes intense changes in the <it>X. fastidiosa </it>transcriptome and some of these differentially expressed genes belong to the σ⁵⁴regulon.</p

A importância de ações educativas e do uso das tecnologias na sala de espera para a promoção da saúde bucal de adultos

Cárie dentária e doença periodontal representam as doenças bucais de maior severidade e prevalência, constituindo problema de saúde pública. Os levantamentos epidemiológicos têm sinalizado dados relevantes sobre a condição da saúde bucal das populações, suas relações com a condição socioeconômica e orientado a implantação de programas de promoção de saúde e prevenção de doenças através de políticas públicas. Este trabalho tem como objetivo salientar a importância de ações educativas e uso de tecnologias para adultos na sala de espera, mediante revisão narrativa de literatura. As relações entre as afecções bucais, fatores de risco e protetores à saúde, eficácia de programas e estratégias mostram a significância dos espaços das salas de espera para uso de recursos como vídeos, utilização de smarthphones, oficinas integrativas e jogos lúdicos. Essas atividades educativas podem proporcionar maior conhecimento sobre os fatores etiológicos das enfermidades bucais,orientação de cuidado e dieta conferindo autonomia e adoção de comportamentos saudáveis para a vida dos indivíduos

A importância de ações educativas e do uso das tecnologias na sala de espera para a promoção da saúde bucal de adultos

Cárie dentária e doença periodontal representam as doenças bucais de maior severidade e prevalência, constituindo problema de saúde pública. Os levantamentos epidemiológicos têm sinalizado dados relevantes sobre a condição da saúde bucal das populações, suas relações com a condição socioeconômica e orientado a implantação de programas de promoção de saúde e prevenção de doenças através de políticas públicas. Este trabalho tem como objetivo salientar a importância de ações educativas e uso de tecnologias para adultos na sala de espera, mediante revisão narrativa de literatura. As relações entre as afecções bucais, fatores de risco e protetores à saúde, eficácia de programas e estratégias mostram a significância dos espaços das salas de espera para uso de recursos como vídeos, utilização de smarthphones, oficinas integrativas e jogos lúdicos. Essas atividades educativas podem proporcionar maior conhecimento sobre os fatores etiológicos das enfermidades bucais,orientação de cuidado e dieta conferindo autonomia e adoção de comportamentos saudáveis para a vida dos indivíduos

The Flagella of an Atypical Enteropathogenic Escherichia coli Strain Are Required for Efficient Interaction with and Stimulation of Interleukin-8 Production by Enterocytes in Vitro

The ability of some typical enteropathogenic Escherichia coli (EPEC) strains to adhere to, invade, and increase interleukin-8 (IL-8) production in intestinal epithelial cells in vitro has been demonstrated. However, few studies regarding these aspects have been performed with atypical EPEC (aEPEC) strains, which are emerging enteropathogens in Brazil. in this study, we evaluated a selected aEPEC strain (1711-4) of serotype O51:H40, the most prevalent aEPEC serotype in Brazil, in regard to its ability to adhere to and invade Caco-2 and T84 cells and to elicit IL-8 production in Caco-2 cells. the role of flagella in aEPEC 1711-4 adhesion, invasion, and IL-8 production was investigated by performing the same experiments with an isogenic aEPEC mutant unable to produce flagellin (FliC), the flagellum protein subunit. We demonstrated that this mutant (fliC mutant) had a marked decrease in the ability to adhere to T84 cells and invade both T84 and Caco-2 cells in gentamicin protection assays and by transmission electron microscopy. in addition, the aEPEC 1711-4 fliC mutant had a reduced ability to stimulate IL-8 production by Caco-2 cells in early (3-h) but not in late (24-h) infections. Our findings demonstrate that flagella of aEPEC 1711-4 are required for efficient adhesion, invasion, and early but not late IL-8 production in intestinal epithelial cells in vitro.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Colegio Doutoral Franco BrasileiroInstitut PasteurFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Programa de Apoio a Nucleos de ExcelenciaPRONEXConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilInst Pasteur, Unite Pathogenie Bacterienne Muqueuses, F-75724 Paris 15, FranceInst Butantan, Bacteriol Lab, BR-05503900 São Paulo, BrazilInst Fleury Ensino & Pesquisa, BR-04344903 São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilInstitut Pasteur: PTR165FAPESP: 05/59128-0Web of Scienc

Análise de habilidades cognitivas exigidas na avaliação do ENADE-Química : um estudo preliminar no ensino superior

O Exame Nacional de Desempenho dos Estudantes (ENADE) é um instrumento pensado para acompanhar o desenvolvimento da educação superior no Brasil e diagnosticar habilidades cognitivas e conhecimentos adquiridos pelos egressos. Neste trabalho são analisadas questões do ENADE 2014 para os cursos de química (formação de professores e bacharelado), organizando-as em um quadro orientador de habilidades, competências, conhecimentos específicos do campo disciplinar, operações cognitivas e seu respectivo nível de dificuldade. Das questões analisadas, identificamos operações cognitivas de diferentes ordens, bem como a presença de textos contextualizadores em algumas questões, mas desnecessários em outras. Ainda que preliminar, entendemos que este estudo pode contribuir para as discussões acerca do projeto político pedagógico dos cursos de química